Add GraphIndexes API manual page

Minor fixes to project files

Author: Ben J. Ward

.github/workflows/TagBot.yml

@@ -0,0 +1,13 @@
+name: TagBot
+on:
+  schedule:
+    - cron: '0 * * * *'
+jobs:
+  TagBot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.TAGBOT_KEY }}
+          registry: BioJulia/BioJuliaRegistry

Project.toml

@@ -4,7 +4,6 @@ authors = ["Ben J. Ward <benjward@protonmail.com>"]
 version = "0.1.0"
 
 [deps]
-Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
 FASTX = "c2308a5c-f048-11e8-3e8a-31650f418d12"
 ReadDatastores = "70a005b8-9d8a-11e9-0d98-c909fa2e52d2"

docs/make.jl

@@ -1,7 +1,7 @@
 using Documenter, GenomeGraphs, Pkg
 
 makedocs(
-    modules = [GenomeGraphs, GenomeGraphs.Graphs, GenomeGraphs.MerTools],
+    modules = [GenomeGraphs, GenomeGraphs.Graphs, GenomeGraphs.MerTools, GenomeGraphs.GraphIndexes],
     format = Documenter.HTML(),
     sitename = "GenomeGraphs.jl",
     authors = replace(join(Pkg.TOML.parsefile("Project.toml")["authors"], ", "), r" <.*?>" => "" ),
@@ -12,7 +12,8 @@ makedocs(
         ],
         "API" => [
             "Graphs submodule" => "api/Graphs.md",
-            "MerTools submodule" => "api/MerTools.md"
+            "MerTools submodule" => "api/MerTools.md",
+            "GraphIndexes submodule" => "api/GraphIndexes.md"
         ]
     ],
 

docs/src/api/GraphIndexes.md

@@ -4,7 +4,31 @@ CurrentModule = GenomeGraphs.GraphIndexes
 
 # API: The GraphIndexes submodule
 
+The GraphIndexes submodule contains some simple indexes and data structures that
+are useful if not required, for the development of mappers and motif/sequence
+finding heuristics.
+
+All types and methods defined in this module are documented here.
+
 !!! note
     This is a reference of an internal sub-module's API for developers and
     experienced users. First ask yourself if what you need isn't covered by
-    the higher-level WorkSpace API. 
+    the higher-level WorkSpace API.
+
+!!! warning
+    This submodule is still under construction.
+
+## Types
+
+```@docs
+UniqueMerIndex
+```
+
+## Public / Safe methods
+
+```@docs
+isunmappable
+find_unique_mer
+```
+
+## Internal / Unsafe methods

src/GFA1/GFA1.jl

@@ -10,6 +10,7 @@ using BioSequences: AbstractMer, position, ksize, fwmer, bwmer, each
 
 using ..Graphs: NodeID, sequence, each_node_id, SequenceDistanceGraph
 
+
 struct GraphStrandPosition
     node::NodeID
     position::UInt32
@@ -18,6 +19,11 @@ end
 Base.summary(io::IO, pos::GraphStrandPosition) = print(io, "(Node: ", pos.node, ", Base position: ", pos.position, ')')
 Base.show(io::IO, pos::GraphStrandPosition) = summary(io, pos)
 
+"""
+An index of all the unique kmers in a graph.
+
+
+"""
 struct UniqueMerIndex{M<:AbstractMer}
     mer_to_graphposition::Dict{M,GraphStrandPosition}
     unique_mers_per_node::Vector{UInt64}

src/GFA1/machines.jl

@@ -900,7 +900,7 @@ function write_to_gfa1(sg::SequenceDistanceGraph, filename::String)
             continue
         end
         println(gfa, "S\tseq", nid, "\t*\tLN:i:", length(n), "\tUR:Z:", fasta_filename)
-        write(fasta, FASTA.Record(string("seq", nid), sequence(n)))
+        write(fasta, FASTA.Record(string("seq", nid), unsafe_sequence(n)))
     end
     close(fasta)
     for ls in links(sg)